Molecular taxonomy of Paracoccus halodenitrificans, Aeromonas salmonicida and Enterococcus seriolicida

The sequence of the 16S rRNA molecule has become accepted as a systematic fingerprint allowing the evolutionary history of an organism and its phylogenetic status at various taxonomic levels to be characterised. Collection of sequence data and their comparison under explicitly defined and widely, though tentatively, accepted algorithms provides much insight into the relationships between organisms. In the study of microbiology, classical taxonomy has been hindered by a paucity of morphological distinction between bacteria. With the acceptance of molecular systematics, many bacteria and groups of bacteria are now being reorganised into a system that reflects both their histories and their relationships, and is consequently more stable than heretofore. This thesis deals with the classification of three bacteria on the basis of their 16S rRNA sequences. * Paracoccus halodenitrifi cans Various chemotaxonomic and molecular data suggest that this species is generically misplaced. 16S rDNA sequence data place the type species, P. denitrificans, in the a-subclass of the Proteobacteria. 16S rDNA sequence analysis undertaken in this work places P. halodenitrifi cans within the family Halomonadaceae in the g-subclass of the Proteobacteria. * Enterococcus seriolicida A bacterial strain isolated from a Tasmanian salmon farm bears strong resemblance to E. seriolicida (ATCC 49156\\(^T\\) = YT-3). In 1993, workers in Spain suggested that E. seriolicida and Lactococcus garvieae are synonymous by 16S rRNA sequence identity, though no sequence data for the former was published. Analysis of the 16S rRNA sequence of E. seriolicida in this work assigns the species to the genus Lactococcus. The sequence of E. seriolicida differs from the published 16S rRNA sequence of L. garvieae in only seven positions. These differences and their significance are discussed. * Aeromonas salmonicida A bacterial strain isolated on a northern Tasmanian fish farm from a skin lesion of the greenback flounder Rhombosolea tapirina was presumed an endemic atypical subspecies of the salmonid pathogen Aeromonas salmonicida. Clarification is necessary for an accurate assessment of its significance for the fishing industry. 16S rRNA sequence of this organism shows 100% identity with that of the species Aeromonas salmonicida subsp. masoucida and achromo genes, despite phenotypic differences between the bacteria. The genus Aeromonas has an unusually high degree of sequence similarity among the 16S rRNA genes of its members. This may make taxonomic clarification by this criterion dubious. The definition of a species on the basis of the sequence of its 16S rRNA molecule has ramifications beyond taxonomy. Synthetic oligonucleotide probes designed to complement specifically unique regions the 16S rRNA or rDNA can rapidly and accurately identify organisms for many purposes. The salmonid industry in Tasmania has been free of the major diseases responsible for devastating losses in overseas fisheries. However, two pathogenic bacteria have been isolated locally, Enterococcus seriolicida and a presumed endemic subspecies of Aeromonas salmonicida. Molecular probes directed against the rDNA of these organisms are required that will allow them to be identified rapidly, their occurrence investigated and their epidemiology traced efficiently should the need arise. A simple diagnostic assay, compatible with normal pathological laboratory routine, is necessary. Therefore these probes have been designed for use as primers in a PCR-based assay.